Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 174 bits (440), Expect = 4e-48 Identities = 108/345 (31%), Positives = 193/345 (55%), Gaps = 41/345 (11%) Query: 6 IEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIM 65 ++ VSK + D+ + L+D + +++ G +++G SGSGKS++L IIAGL + G + Sbjct: 4 LKVSEVSKRY-DAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVH 62 Query: 66 LDGVRINDIPTNKR-----DVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAE 120 L +I + P K ++ + Q Y L+P+ V EN+A PL L DK ++R AE Sbjct: 63 LGDQKILN-PAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERTAE 119 Query: 121 VLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYEL 180 +L+++ L ++ + R+LSGGQ+Q+VAI RA+ +P V+LLDEP S+LD + D+ EL Sbjct: 120 ILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEEL 179 Query: 181 RELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGE 240 +E+ L +T +FVTHD ++AL MS+ + ++ G+++Q G +++ +P + +VA G Sbjct: 180 KEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGY 239 Query: 241 SNILPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGKLQVKVDTQ 300 N++PG E +RP +++IT + ++ +V Q Sbjct: 240 LNLIPGA--------------------------EEAYVRPSEVKIT--SKTSIKAEVVKQ 271 Query: 301 LFRGVHYEIIAYDELGNE--WMIHSTRKAI-VGEEIGLDFEPEDI 342 F +HY ++ +E W + +++ VG+E+ LD++ E + Sbjct: 272 QFL-IHYNLLTVKLEDSELFWKVDDPSRSVNVGDEVFLDYQKEQL 315 Lambda K H 0.318 0.138 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 295 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 385 Length of database: 318 Length adjustment: 29 Effective length of query: 356 Effective length of database: 289 Effective search space: 102884 Effective search space used: 102884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory